First-half goals from Albert Rusnak and Abdul Razak did the damage on a morale-boosting afternoon for the boy Blues.
After the senior side just about dispatched Wigan in the Premier League two nights previously, it was Attilio Lombardo’s under-21 selection’s turn to take on the Latics on a bright spring day at their Christopher Park training ground.
City booked their place in this Lancashire Senior cup quarter-final with a penalty shoot-out win over Blackpool back in February.
It was City Elite Development Squad’s second game in 24 hours, so unsurprisingly wholesale changes were made from the team that lost to Bolton in Leyland on Thursday night.
Only Reece Wabara survived in the starting XI, with ten making way for a line-up that more closely resembled a regular EDS side.
That allowed John Guidetti to lead the line with his freshly-shaved head (the result of a botched hair dye attempt), with Denis Suarez, Marcos Lopes and Albert Rusnak in support.
Abdul Razak also lent his Ivorian steel to the base of midfield, alongside the in-form Wales u21 international Emyr Huws.
Anyone present at the Etihad Stadium on Wednesday night will be familiar with the expansive, attractive brand of football favoured by the Latics under Roberto Martinez and from the evidence of Wigan’s start; it’s a policy that extends down the age-groups.
The home side settled into their game quicker on a carpet-like surface, exchanging possession with one another fluently and not giving City’s diminutive attacking midfielders a second to settle on the ball.
Wigan were able to name Daniel Redmond, son of City Academy graduate Steve, in their attack, and the youngster was first to trouble either goal with a powerful effort from 25 yards which whistled an inch past Ian Lawlor’s post on 15 minutes.
Redmond went close again two minutes later when he was played through but Lawlor was out quickly to narrow the angle and the Wigan man side-footed past the post.
City were forced to adopt a more direct approach in these early stages as a reaction to the home side’s pressing game, looking longer to the totem of Guidetti in his traditional no.9 role to hold up the ball to give teammates time to get forward.
However, when City finally did warm to the task around the 25-minute mark, some of their interplay was sublime.
As it was when they took a 33rd minute lead.
A good ball in from Wabara was made great by an instinctive back-heel from Guidetti which rolled into the path of Lopes, who delivered a measured cut-back for Rusnak to side-foot City into the lead.
That goal gave the away side a confidence boost and all-of-a-sudden it seemed that every one of their flicks, one-twos and intricate turns was coming off.
Guidetti was again involved when City extended their lead with one of the last kicks of the first-half as the Swede turned the ball into the path of Razak who unleashed a vicious, drilled effort from 25-yards which nestled satisfyingly into the bottom corner of the net.
With one foot in the semi-finals of the Lancashire Senior Cup, City sured things up in the second half and employed a more patient approach, limiting their opponents' space, though always ready to launch their own counter raids.
This blueprint nearly finished the game off on the hour mark when Suarez danced his way through the Latics defence but Marko Marosi sprinted off his line and smothered at the feet of the Spanish u20 international.
Against Newcastle last time this selection assembled, City let a lead slip when in the ascendency but Lombardo took no chances this time around and withdrew Lopes for Olivier Ntcham to give his men an extra injection of physicality in the midfield third.
Unlike that meeting with the Magpies, City held firm this time and never looked in any danger of silly concessions, holding out to win comfortably by a two-goal margin with the extra bonus of a clean sheet.
They will meet Rochdale away from home in the semi-finals of the Lancashire Senior Cup on a date to be confirmed.